Transposable elements (TEs) constitute a substantial fraction of the eukaryotic genome and, as a result, have a complex relationship with their host that is both adversarial and dependent. To minimize damage to cellular genes, TEs possess mechanisms that target integration to sequences of low importance. However, the retrotransposon Tf1 of Schizosaccharomyces pombe integrates with a surprising bias for promoter sequences of stress-response genes. The clustering of integration in specific promoters suggests that Tf1 possesses a targeting mechanism that is important for evolutionary adaptation to changes in environment. We report here that Sap1, an essential DNA-binding protein, plays an important role in Tf1 integration. A mutation in Sap1 resulted in a 10-fold drop in Tf1 transposition, and measures of transposon intermediates support the argument that the defect occurred in the process of integration. Published ChIP-Seq data on Sap1 binding combined with high-density maps of Tf1 integration that measure independent insertions at single-nucleotide positions show that 73.4% of all integration occurs at genomic sequences bound by Sap1. This represents high selectivity because Sap1 binds just 6.8% of the genome. A genome-wide analysis of promoter sequences revealed that Sap1 binding and amounts of integration correlate strongly. More important, an alignment of the DNA-binding motif of Sap1 revealed integration clustered on both sides of the motif and showed high levels specifically at positions +19 and 29. These data indicate that Sap1 contributes to the efficiency and position of Tf1 integration. KEYWORDS Sap1; Tf1; integration; transposition; Schizosaccharomyces pombe R ETROTRANSPOSONS are pervasive among eukaryotes and, in many cases, account for a substantial portion of the host genome (Moore et al. 2004;Scheifele et al. 2009;Levin and Moran 2011). The ability of these elements to selectively integrate into specific target sequences has been paramount to their success because the employment of specific targeting mechanisms has allowed these retrotransposons to propagate within host genomes without disrupting genes and compromising the host's survival (Levin and Moran 2011). The long terminal repeat (LTR) retrotransposons Ty1, Ty3, and Ty5 of Saccharomyces cerevisiae avoid causing damage to the host by targeting noncoding genomic regions; Ty1 and Ty3 integrate upstream of RNA polemerase III-transcribed genes, while Ty5 integrates into heterochromatin (Chalker and Sandmeyer 1990;1992;Ji et al. 1993;Kirchner et al. 1995;Devine and Boeke 1996;Zou et al. 1996;Zou and Voytas 1997;Yieh et al. 2000;Sandmeyer 2003;Lesage and Todeschini 2005).In Schizosaccharomyces pombe, the LTR retrotransposon Tf1 has a unique targeting mechanism that directs integration to promoters of RNA polymerase II-transcribed genes with a bias for the promoters of stress-response genes (Behrens et al. 2000;Singleton and Levin 2002;Bowen et al. 2003;Leem et al. 2008;Guo and Levin 2010). Surprisingly, insertion of Tf1 into promoters rarel...

No abstract

Long terminal repeat (LTR) retrotransposons are closely related to retroviruses and, as such, are important models for the study of viral integration and target site selection. The transposon Tf1 of Schizosaccharomyces pombe integrates with a strong preference for the promoters of polymerase II (Pol II)-transcribed genes. Previous work in vivo with plasmid-based targets revealed that the patterns of insertion were promoter specific and highly reproducible. To determine which features of promoters are recognized by Tf1, we studied integration in a promoter that has been characterized. The promoter of fbp1 has two upstream activating sequences, UAS1 and UAS2. We found that integration was targeted to two windows, one 180 nucleotides (nt) upstream and the other 30 to 40 nt downstream of UAS1. A series of deletions in the promoter showed that the integration activities of these two regions functioned autonomously. Integration assays of UAS2 and of a synthetic promoter demonstrated that strong promoter activity alone was not sufficient to direct integration. The factors that modulate the transcription activities of UAS1 and UAS2 include the activators Atf1p, Pcr1p, and Rst2p as well as the repressors Tup11p, Tup12p, and Pka1p. Strains lacking each of these proteins revealed that Atf1p alone mediated the sites of integration. These data indicate that Atf1p plays a direct and specific role in targeting integration in the promoter of fbp1.